FourFourTwo magazine revealed on 28 July 2007 that after the Asian Cup Milligan had gone without Sydney FC's permission to trial for teams in Europe.

The following day Milligan reportedly walked out on Metz just before a scheduled trial game appearance against Standard Liège, allegedly out of frustration at the right-back position he would be trialled in.

[8][9] During the summer of 2008, he was linked with a move to English Premier League clubs Blackburn Rovers, Manchester City and Arsenal, RC Lens of Ligue 1, as well as with FC Porto in the Primeira Liga and Bundesliga side Werder Bremen.

On 21 October 2008, The Sydney Morning Herald reported that Milligan had signed a guest contract with Newcastle United Jets for seven weeks.

[10] On 19 May, Milligan scored his first goal for Shanghai Shenhua in their 1–1 draw in the AFC Champions League group stage match against Kashima Antlers.

[11] When the 2011 Tōhoku earthquake and tsunami struck Japan, Milligan decided to flee the country, fearing for the safety of not only himself, but his wife and child.

[12] With the J2 League suspended until further notice, JEF United Chiba gave permission for Milligan to train in a bid to keep his fitness up with his former A-League club Sydney FC.

[17] Milligan starred for Melbourne Victory during their 2012–13 season, moving from centre-back to play as a defensive midfielder, and quickly established himself as one of the best players in the league.

On 17 May 2015, Milligan captained his side during their 3–0 defeat of Sydney FC in the 2014–15 A-League Grand Final, held at AAMI Park, Melbourne, and was awarded the Joe Marston Medal as the best player in the match.

[26] Hibernian head coach Paul Heckingbottom said that he had opted to exercise a break clause in Milligan's contract as he wanted to "recruit something different to play in that position".

[29] On 30 July 2020, following his release from Southend, Milligan returned home to Australia to join newly formed A-League club Macarthur FC, signing a two-year deal.

He made his senior international debut against Liechtenstein on 7 June 2006, coming off the bench in the 85th minute of Australia's last warm-up game before the World Cup.

During the tournament, Milligan was selected to play in the starting line-up for Australia against co-host nation Thailand in the final game of the group matches.

Australia won 4–0 and advanced to the quarter finals of the competition with Milligan putting in what was widely regarded as a Man of the Match performance in the centre of a three-man defence.

On 21 July 2007, in the quarter-final against Japan, Milligan was unfortunate in failing to clear a ball from the penalty area that saw striker Naohiro Takahara pounce and score an equaliser.

Milligan scored his first international goal for the Socceroos against Indonesia in a 2011 Asian Cup Qualifiers played at Suncorp Stadium in Brisbane.

His 2010 FIFA World Cup profile described him as "[a] mobile defender with good ball skills and an ability to play a raking pass.

[37] He played alongside James Troisi and captain Mile Jedinak in a three-man midfield in the Socceroos warm-up match vs Croatia.